Mercurial > repos > iuc > bcftools_consensus

comparison bcftools_consensus.xml @ 23:5970245e8525 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bfc4ff4956b94885638ae07a2560bac5f84fcca8
author iuc
date Tue, 16 Jul 2024 16:51:47 +0000
parents 99550ee60e65
children 62ed6ee05b6f
comparison
equal deleted inserted replaced
22:f86b9f21af7f 23:5970245e8525
137 <data name="chain_file" format="txt" label="${tool.name} on ${on_string}: chain"> 137 <data name="chain_file" format="txt" label="${tool.name} on ${on_string}: chain">
138 <filter>chain</filter> 138 <filter>chain</filter>
139 </data> 139 </data>
140 </outputs> 140 </outputs>
141 <tests> 141 <tests>
142 <test> 142 <test expect_num_outputs="2">
143 <expand macro="test_using_reference" ref="consensus.fa" /> 143 <expand macro="test_using_reference" ref="consensus.fa" />
144 <param name="input_file" ftype="vcf" value="consensus.vcf" /> 144 <param name="input_file" ftype="vcf" value="consensus.vcf" />
145 <param name="mask" ftype="tabular" value="consensus.tab" /> 145 <param name="mask" ftype="tabular" value="consensus.tab" />
146 <param name="chain" value="True" /> 146 <param name="chain" value="True" />
147 <output name="output_file"> 147 <output name="output_file">
153 <assert_contents> 153 <assert_contents>
154 <has_text text="chain 497 1 501 + 1 501 1 502 + 1 502 1" /> 154 <has_text text="chain 497 1 501 + 1 501 1 502 + 1 502 1" />
155 </assert_contents> 155 </assert_contents>
156 </output> 156 </output>
157 </test> 157 </test>
158 <test> 158 <test expect_num_outputs="2">
159 <expand macro="test_using_reference" select_from="cached" ref="consensus" /> 159 <expand macro="test_using_reference" select_from="cached" ref="consensus" />
160 <param name="input_file" ftype="vcf" dbkey="?" value="consensus.vcf" /> 160 <param name="input_file" ftype="vcf" dbkey="?" value="consensus.vcf" />
161 <param name="mask" ftype="tabular" value="consensus.tab" /> 161 <param name="mask" ftype="tabular" value="consensus.tab" />
162 <param name="chain" value="True" /> 162 <param name="chain" value="True" />
163 <output name="output_file"> 163 <output name="output_file">
169 <assert_contents> 169 <assert_contents>
170 <has_text text="chain 497 1 501 + 1 501 1 502 + 1 502 1" /> 170 <has_text text="chain 497 1 501 + 1 501 1 502 + 1 502 1" />
171 </assert_contents> 171 </assert_contents>
172 </output> 172 </output>
173 </test> 173 </test>
174 <test> 174 <test expect_num_outputs="1">
175 <expand macro="test_using_reference" ref="consensus.fa" /> 175 <expand macro="test_using_reference" ref="consensus.fa" />
176 <param name="input_file" ftype="vcf" value="consensus.vcf" /> 176 <param name="input_file" ftype="vcf" value="consensus.vcf" />
177 <param name="mask" ftype="tabular" value="consensus.tab" /> 177 <param name="mask" ftype="tabular" value="consensus.tab" />
178 <param name="chain" value="False" /> 178 <param name="chain" value="False" />
179 <param name="rename" value="True" /> 179 <param name="rename" value="True" />
184 <assert_contents> 184 <assert_contents>
185 <has_text text=">consensus.vcf-2" /> 185 <has_text text=">consensus.vcf-2" />
186 </assert_contents> 186 </assert_contents>
187 </output> 187 </output>
188 </test> 188 </test>
189 <test> 189 <test expect_num_outputs="1">
190 <expand macro="test_using_reference" ref="consensus.fa" /> 190 <expand macro="test_using_reference" ref="consensus.fa" />
191 <param name="input_file" ftype="vcf" value="consensus.vcf" /> 191 <param name="input_file" ftype="vcf" value="consensus.vcf" />
192 <section name="sec_restrict"> 192 <section name="sec_restrict">
193 <param name="include" value='TYPE="snp"' /> 193 <param name="include" value='TYPE="snp"' />
194 </section> 194 </section>
197 <has_text text="TACAAAATATGACATATCAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTTGA" /> 197 <has_text text="TACAAAATATGACATATCAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTTGA" />
198 </assert_contents> 198 </assert_contents>
199 </output> 199 </output>
200 </test> 200 </test>
201 <!--Test absent option--> 201 <!--Test absent option-->
202 <test> 202 <test expect_num_outputs="1">
203 <expand macro="test_using_reference" ref="consensus.fa" /> 203 <expand macro="test_using_reference" ref="consensus.fa" />
204 <param name="input_file" ftype="vcf" value="consensus.vcf" /> 204 <param name="input_file" ftype="vcf" value="consensus.vcf" />
205 <section name="sec_restrict"> 205 <section name="sec_restrict">
206 <param name="include" value='TYPE="snp"' /> 206 <param name="include" value='TYPE="snp"' />
207 </section> 207 </section>
214 <assert_command> 214 <assert_command>
215 <has_text text="--absent" /> 215 <has_text text="--absent" />
216 </assert_command> 216 </assert_command>
217 </test> 217 </test>
218 <!--Test mask options --> 218 <!--Test mask options -->
219 <test> 219 <test expect_num_outputs="1">
220 <expand macro="test_using_reference" ref="consensus.fa" /> 220 <expand macro="test_using_reference" ref="consensus.fa" />
221 <param name="input_file" ftype="vcf" value="consensus.vcf" /> 221 <param name="input_file" ftype="vcf" value="consensus.vcf" />
222 <section name="sec_restrict"> 222 <section name="sec_restrict">
223 <param name="include" value='TYPE="snp"' /> 223 <param name="include" value='TYPE="snp"' />
224 </section> 224 </section>